Nomenclature

The nomenclature for phycobiliproteins can be somewhat confusing and reflects, in part, historical developments in the study of phycobiliproteins. PCs and PEs were all originally given the prefix C- or R- to designate whether they were purified from cyanophytes (cyanobacteria) or rho-dophytes (red algae). The designation B-was later introduced for a distinct type of PE from the red alga Smithora naiadum, which is a member of the order Bangiales (1,37). The three major types of Class I PE (those that contain five bilins per aP monomer; see below) differ in their absorbance properties due to the types of

Figure 1. Structures of the four singly-linked peptide-linked bilins present in the phycobiliproteins of cyanobacteria. The numbering scheme for the carbon atoms is indicated.

bilins present on their aP subunits. These proteins exhibit one, two, or three distinct peaks in the visible region of the spectrum and are called C-phycoerythrin (C-PE; containing only PEB), B-phycoerythrin (B-PE), and R-phycoerythrin (R-PE), respectively, regardless of the group from which they have been isolated (References 33, 37, and references therein). These designations seemed sufficient until marine unicellular cyanobacteria were shown to contain two forms of PE, PE I, and PE II, in the rods of their phycobilisomes (55, 67). PE I was less abundant than PE II. PE II has an extra bilin (PUB) on the a subunit (a-75) and contains both PEB and PUB. Thus far, only two Synechococcus strains (WH8020 and WH8103) have been shown to contain a PE with six chro-mophores per aP monomer (55). Therefore, these two PEs are members of a new class of PE, dubbed Class II PE. However, PE I is more like other PEs that have been characterized, in that it contains only five bilins per aP monomer and contains either only PEB or both PEB and PUB (55). Thus far, no red algal PE has been shown to be a member of Class II PE. B-PE, R-PE, and PE II complexes carry bilins on their associated linker protein, called y (34, 45). A recently discovered red algal PE (from Audouinella macrospora) contains a PE with PCB, PEB, and PUB chro-mophores and is more like B- and R-PEs in that it contains 5 bilins per aP monomer and has bilins present on its y subunit (29). This PE is a Class I member, but is not by definition an R-PE, which have been shown to contain PUB and PEB that contribute to the three absorption peaks in the visible region.

Four major types of PC have been characterized (15,63), and all PC types contain PCB as the terminal acceptor bilin at cysteine P-82. C-PC contains PCB at all three cysteines (25,46,60). R-PC-I, present in some red algae including Porphyridium cru-

entum, contains PEB at cysteine P-155 and PCB at the other two positions (33). R-PC II, isolated from several unicellular marine cyanobacterial strains, contains PEB at cysteines a-84 and P-155 and PCB at cysteine P-82 (55,56). R-PC-III was isolated from Synechococcus sp. WH7805 and has a PCB:PEB ratio of 2:1, but differences in the absorption properties of this PC suggest that the chromophores are distributed differently than in R-PC-I (57). The fourth form of PC, R-PC-IV, was isolated from Synechococcus sp. WH8501 and was found to contain PUB attached at a-84 and PCB at the other two positions on the P subunit (67). Finally, PEC is structurally more similar to PCs than to PEs, but is found distal to PC in the phycobilisome rods of some cyanobacterial strains. PEC carries PXB at a-84 and PCB at both positions on the P subunit (9,12). Spectroscopic variants of AP (which contains one PCB on each subunit) have not yet been identified. Thus, the nomenclature for biliproteins devised previously has been rather haphazard and confusing. A new form of nomenclature has been suggested (51), but has not been widely used thus far.

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